1-41871577-T-G

Variant names:

• chr1-41871577-T-G
• rs710229
• NM_024503.5:c.-801+46836A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024503.5(HIVEP3):​c.-801+46836A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 152,272 control chromosomes in the GnomAD database, including 57,748 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.87 (57748 hom., cov: 33)
• Consequence: HIVEP3 NM_024503.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 2 publications found

Genes affected

HIVEP3 (HGNC:13561): (HIVEP zinc finger 3) This gene encodes a member of the human immunodeficiency virus type 1 enhancer-binding protein family. Members of this protein family contain multiple zinc finger and acid-rich (ZAS) domains and serine-threonine rich regions. This protein acts as a transcription factor and is able to regulate nuclear factor kappaB-mediated transcription by binding the kappaB motif in target genes. This protein also binds the recombination signal sequence that flanks the V, D, and J regions of immunoglobulin and T-cell receptors. Alternate splicing results in both coding and non-coding transcript variants. [provided by RefSeq, Sep 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024503.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIVEP3	NM_024503.5	MANE Select	c.-801+46836A>C		intron	N/A	NP_078779.2	Q5T1R4-1
	HIVEP3	NM_001127714.3		c.-721+46836A>C		intron	N/A	NP_001121186.1	Q5T1R4-2
	HIVEP3	NR_038260.2		n.511-22488A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIVEP3	ENST00000372583.6	TSL:1 MANE Select	c.-801+46836A>C		intron	N/A	ENSP00000361664.1	Q5T1R4-1
	HIVEP3	ENST00000372584.5	TSL:1	c.-721+46836A>C		intron	N/A	ENSP00000361665.1	Q5T1R4-2
	HIVEP3	ENST00000489103.5	TSL:1	n.232-22488A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.868 AC: 132127 AN: 152154 Hom.: 57696 Cov.: 33

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.843

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.868 AC: 132238 AN: 152272 Hom.: 57748 Cov.: 33 AF XY: 0.869 AC XY: 64700 AN XY: 74442

African (AFR) AF: 0.964 AC: 40087 AN: 41568

American (AMR) AF: 0.813 AC: 12432 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2937 AN: 3466

East Asian (EAS) AF: 0.997 AC: 5177 AN: 5192

South Asian (SAS) AF: 0.853 AC: 4114 AN: 4824

European-Finnish (FIN) AF: 0.826 AC: 8739 AN: 10580

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55980 AN: 68022

Other (OTH) AF: 0.845 AC: 1786 AN: 2114

Alfa AF: 0.858 Hom.: 7290

Bravo AF: 0.870

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.71
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs710229; hg19: chr1-42337248;